Publications

2019

  • Yang X, Cheng H, Chen J, Wang R, Saleh A, Si H, Lee S, Guven-Maiorov E, Keskin O, Gursoy A, Nussinov R, Fang J, Waes CV, Chen Z, Head and Neck Cancers Promote an Inflammatory Transcriptome through Coactivation of Classic and Alternative NF-κB Pathways, Cancer Immunology Research, Volume 7, November 2019, Pages 1760-1774
  • Dincer C, Kaya T, Keskin O, Gursoy A, Tuncbag N, 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients, PLoS computational biology, Volume 15, 2019
  • Ozdemir ES, Nussinov R, Gursoy A,  Keskin O, Developments in integrative modeling with dynamical interfaces, Current Opinion in Structural Biology, Volume 56, June 2019, Pages 11-17
  • Uba AI, Weako J, Keskin O, Gürsoy A, Yelekçi K, Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation, Journal of Biomolecular Structure and Dynamics, 2019, Pages 1-10.
  • Cavga AD, Tardu M, Korkmaz T, Keskin O, Ozturk N, Gursoy A, Kavakli IH., Cryptochrome deletion in p53 mutant mice enhances apoptotic and anti-tumorigenic responses to UV damage at the transcriptome level, Functional & integrative genomics, Volume 19, 2019, Pages 729–742.
  • Balci AT, Gumeli C, Hakouz A,Yuret A, Keskin O.,DeepInterface: Protein-protein interface validation using 3D Convolutional Neural Networks, bioRxiv,
  • Ozdemir ES, Nussinov R, Gursoy A, Keskin O., Developments in integrative modeling with dynamical interfaces, Current Opinion in Structural Biology, Vol 56, 2019,Pages 11-17.

2018

  • Ozdemir ES, Gursoy A, Keskin O., Analysis of single amino acid variations in singlet hot spots of protein–protein interfaces,  Bioinformatics 34 (17), i795-i801
  • Ozdemir ES, Jang H, Gursoy A, Keskin O, Li Z, Sacks DB, Nussinov R., Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2, J Biol Chem. 2018 Mar 9;293(10):3685-3699.
  • Ozdemir ES, Jang H, Gursoy A, Keskin O, Nussinov R., Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEδ, J Phys Chem B. 2018 Aug 2;122(30):7503-7513.

2017

  • Halakou F.,  Kilic E.S, Cukuroglu E., Keskin O.,  Gursoy A.,  Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins,  Sci Rep. 2017; 7: 7180.
  • Muratcioglu S, Jang H, Gursoy A, Keskin O, Nussinov R.,  PDEδ Binding to Ras Isoforms Provides a Route to Proper Membrane Localization,  J Phys Chem B. 2017 Jun 22;121(24):5917-5927.
  • Ozgur B, Ozdemir ES, Gursoy A, Keskin O.,  Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations, J Phys Chem B. 2017 Apr 20;121(15):3686-3700.
  • Tuncbag N, Keskin O, Nussinov R, Gursoy A., Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information, Methods Mol Biol. 2017;1558:255-270.
  • Halakou F, Gursoy A, Kilic ES, Keskin O., Topological, functional, and structural analyses of protein-protein interaction networks of breast cancer lung and brain metastases,  2017 EEE Conference Computational Intelligence in Bioinformatics and Computational Biology (CIBCB).
  • Morova T, Gönen M, A Gursoy, Keskin K, Nathan AL., Androgen receptor binding sites are highly mutated in prostate cancer, bioRxiv, 225433, 2017

2016

  • Kuzu G, Keskin O, Nussinov R, Gursoy A., PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.  Acta Crystallogr D Struct Biol. 2016 Oct 1;72(Pt 10):1137-1148.
  • Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R., TRAF3 signaling: Competitive binding and evolvability of adaptive viral molecular mimicry., Biochim Biophys Acta. 2016 Nov;1860(11 Pt B):2646-55.
  • Tuncbag N, Gursoy A, Keskin O, Nussinov R., The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology., Expert Rev Proteomics. 2016 May;13(5):447-9.
  • Keskin O, Tuncbag N, Gursoy A., Keskin O, Tuncbag N, Gursoy A., Chem Rev. 2016 Apr 27;116(8):4884-909.
  • Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R., Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers., Biochem J. 2016 Jun 15;473(12):1719-32.
  • Chavan TS, Muratcioglu S, Marszalek R, Jang H, Keskin O, Gursoy A, Nussinov R, Gaponenko V.,  Plasma membrane regulates Ras signaling networks. Cell Logist. 2016 Feb 18;5(4):e1136374.
  • Nussinov R, Muratcioglu S, Tsai CJ, Jang H, Gursoy A, Keskin O., K-Ras4B/calmodulin/PI3Kα: A promising new adenocarcinoma-specific drug target?,  Expert Opin Ther Targets. 2016 Jul;20(7):831-42.
  • Lu S, Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R, Zhang J.,  Ras Conformational Ensembles, Allostery, and Signaling., Chem Rev. 2016 Jun 8;116(11):6607-65.

2015

  • Muratcioglu S, Guven-Maiorov E, Keskin O, Gursoy A., Advances in template-based protein docking by utilizing interfaces towards completing structural interactomeCurr Opin Struct Biol. 2015 Nov 2;35:87-92.
  • Muratcioglu S, Presman DM, Pooley JR, Grntved L, Hager GL, Nussinov R, Keskin O, Gursoy A., Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP,Biophys J. 2015 Sep 15;109(6):1227-39.
  • Guven-Maiorov E, Keskin O, Gursoy A, Nussinov R., A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory PathwayBiophys J. 2015 Sep 15;109(6):1214-26.
  • Nussinov R, Muratcioglu S, Tsai CJ, Jang H, Gursoy A, Keskin O., The Key Role of Calmodulin in KRAS-Driven AdenocarcinomasMol Cancer Res. 2015 Sep;13(9):1265-73.
  • Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R., The Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling PathwaySci Rep. 2015 Aug 21;5:13128
  • Muratcioglu S, Chavan TS, Freed BC, Jang H, Khavrutskii L, Freed RN, Dyba MA, Stefanisko K, Tarasov SG, Gursoy A, Keskin O, Tarasova NI, Gaponenko V, Nussinov R., GTP- Dependent K-Ras DimerizationStructure. 2015 Jul 7;23(7):1325-35.
  • Cavga AD, Karahan N, Keskin O, Gursoy A., Taming Oncogenic Signaling at Protein Interfaces: Challenges and OpportunitiesCurr Top Med Chem. 2015;15(20):2005-18.
  • Nussinov R, Tsai CJ, Muratcioglu S, Jang H, Gursoy A, Keskin O., Principles of K-Ras effector organization and the role of oncogenic K-Ras in cancer initiation through G1 cell cycle deregulation. Expert Rev Proteomics. 2015 Dec;12(6):669-82

2014

  • Baspinar A, Cukuroglu E, Nussinov R, Keskin O, Gursoy A., PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexesNucleic Acids Res. 2014 Jul;42(Web Server issue):W285-9.
  • Acuner Ozbabacan SE, Gursoy A, Nussinov R, Keskin O. The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and CancerPLoS Comput Biol. 2014 Feb 13;10(2).
  • Cukuroglu E, Gursoy A, Nussinov R, Keskin O. Non-redundant unique interface structures as templates for modeling protein interactionsPLoS One. 2014 Jan 27;9(1).
  • Kuzu G, Keskin O, Nussinov R, Gursoy A. Modeling protein assemblies in the proteomeMol Cell Proteomics. 2014 Mar;13(3):887-96.
  • Guven-Maiorov E, Acuner-Ozbabacan SE, Keskin O, Gursoy A, Nussinov R., Structural pathways of cytokines may illuminate their roles in regulation of cancer development and immunotherapyCancers (Basel). 2014 Mar 25;6(2):663-83.
  • Acuner-Ozbabacan ES, Engin BH, Guven-Maiorov E, Kuzu G, Muratcioglu S, Baspinar A, Chen Z, Van Waes C, Gursoy A, Keskin O, Nussinov R., The structural network of Interleukin-10 and its implications in inflammation and cancerBMC Genomics. 2014;15 Suppl 4:S2. doi: 10.1186/1471-2164-15-S4-S2.
  • Cukuroglu E, Engin HB, Gursoy A, Keskin O., Hot spots in protein-protein interfaces: towards drug discovery. Prog Biophys Mol Biol. 2014 Nov-Dec;116(2-3):165-73
  • Demircioglu D, Keskin O, Gursoy A., Modeling structural protein interaction networks for betweenness analysis. ISCIS2014 LCNS. 2014:367-76

2013

  • Engin HB, Guney E, Keskin O, Oliva B, Gursoy A.,  Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancerPLoS One. 2013 Nov 22;8(11)
  • Maiorov EG, Keskin O, Ng OH, Ozbek U, Gursoy A.,  Identification of interconnected markers for T-cell acute lymphoblastic leukemiaBiomed Res Int. 2013;2013:210253.
  • Engin HB, Gursoy A, Nussinov R, Keskin O. , Network-Based Strategies Can Help Mono- and Poly-pharmacology Drug Discovery: A Systems Biology View. Curr Pharm Des. 2013 May 22.
  • Guven Maiorov E, Keskin O, Gursoy A, Nussinov R. , The structural network of inflammation and cancer: merits and challengesSemin Cancer Biol. 2013 Aug;23(4):243-51.
  • An O, Gursoy A, Gurgey A, Keskin O. , Structural and functional analysis of perforin mutations in association with clinical data of familial hemophagocytic lymphohistiocytosis type 2 (FHL2) patientsProtein Sci. 2013 Jun;22(6):823-39.
  • Kuzu G, Gursoy A, Nussinov R, Keskin O. , Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scaleJ Proteome Res. 2013 Jun 7;12(6):2641-53.
  • Kar G, Keskin O, Fraternali F, Gursoy A. , Emerging role of the ubiquitin-proteasome system as drug targets. Curr Pharm Des. 2013;19(18):3175-89.

2012

  • Engin HB, Keskin O, Nussinov R, Gursoy A., A strategy based on protein-protein interface motifs may help in identifying drug off-targetsJ Chem Inf Model. 2012, Aug 27;52(8):2273-86
  • Kar G, Kuzu G, Keskin O, Gursoy A. , Protein-protein interfaces integrated into interaction networks: implications on drug designCurr Pharm Des. 2012 May 29.
  • Kuzu G, Keskin O, Gursoy A, Nussinov R. Constructing structural networks of signaling pathways on the proteome scale. Curr Opin Struct Biol. 2012 Jun;22(3):367-77.
  • Acuner Ozbabacan SE, Keskin O, Nussinov R, Gursoy A. , Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes. J Struct Biol. 2012 Sep;179(3):338-46
  • Tuncbag N, Keskin O, Nussinov R, Gursoy A. Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement. Proteins. 2012 Apr;80(4):1239-49.
  • Kuzu G, Keskin O, Gursoy A, Nussinov R. Expanding the conformational selection paradigm in protein-ligand dockingMethods Mol Biol. 2012;819:59-74.
  • Kar G, Keskin O, Nussinov R, Gursoy A. Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. J Proteome Res. 2012; Feb 3;11(2):1196-207.

2011

  • N. Tuncbag, A. Gursoy, R. Nussinov, O. Keskin, Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISMNature Protocol, 2011 vol. 6 (9) pp. 1341-54.
  • Cukuroglu E, Gursoy A, Keskin O. HotRegion: a database of predicted hot spot clusters. Nucleic Acids Res. 2012 Jan;40(Database issue):D829-33.
  • Sanli D, Keskin O, Gursoy A, Erman B. Structural cooperativity in histone H3 tail modificationsProtein Sci. 2011 Dec;20(12):1982-90. doi: 10.1002/pro.745.
  • O. Ulucan, O. Keskin, B. Erman, A. Gursoy, A Comparative Molecular Dynamics Study of Methylation State Specificity of JMJD2APLos ONE, 2011 vol. 6 (9) pp. e24664
  • S.E.A. Ozbabacan, H.B. Engin, A. Gursoy, O. Keskin, Transient protein-protein interactionsProtein Engineering Design & Selection, 2011 vol. 24 (9) pp. 635-48.
  • N. Tuncbag, A. Gursoy, O. Keskin, Prediction of protein-protein interactions: unifying evolution and structure at protein interfacesPhys Biol, 2011 vol. 8 (3) pp. 035006.
  • M. Ozboyaci, A. Gursoy, B. Erman, O. Keskin, Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations studyPLos ONE, 2011 vol. 6 (3) pp. e14765.

2010

  • G. Kar, O. Keskin, A. Gursoy, N. Nussinov, Allostery and population shift in drug discoveryCurrent Opinion in Pharmacology, Sep, 2010.
  • S.E.A Ozbabacan, A. Gursoy, O. Keskin, R. Nussinov, Conformational ensembles, signal transduction and residue hot spots: Application to drug discoveryCurrent Opinion in Drug Discovery and Development, 13(5), pp. 527-537, 2010
  • S. Kalyoncu, O. Keskin, A. Gursoy,Interaction prediction and classification of PDZ domainsBMC Bioinformatics, 11(357), 2010.
  • N. Tuncbag, FS. Salman, O. Keskin, A. Gursoy, Analysis and network representation of hotspots in protein interfaces using minimum cut treesProtein-Structure Function and Bioinformatics, 78(10), pp. 2283-2294, 2010.
  • EB. Unal, A. Gursoy, B. Erman,VitAL: Viterbi algorithm for de novo peptide designPLOS One, 5(6), e10926, 2010.
  • N. Tuncbag, O.Keskin, A. Gursoy, HotPoint: hotspot prediction server for protein interfacesNucl. Acids. Res. (38) Web Server Issue, W402-W406, 2010.
  • E. Cukuroglu, A. Gursoy, O. Keskin, Analysis of Hot Region Organization in Hub ProteinsAnnals of Biomedical Engineering, 38(6), pp. 2068-2078, 2010.

2009

  • G. Kar, A. Gursoy, O. Keskin, Human cancer protein-protein interaction network: a structural perspectivePLOS Computational Biology, 5(12) , e1000601, Dec 2009
  • Tuncbag N, Kar G, Gursoy A, Keskin O,  Nussinov R, Towards inferring time dimensionality in protein_protein interaction networks by integrating structures: the p53 exampleMolecular BioSystems, 2009
  • Unal B, Gursoy A, Erman B, Conformational energies and entropies of peptides, and the peptide-protein binding problemPhysical Biology 6, 2009
  • Tuncbag N, Gursoy A, Keskin O, Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracyBioinformatics, Volume: 25 Issue: 12 Pages: 1513-1520 , 2009
  • Tuncbag N, Kar G, Keskin O, Gursoy A, Nussinov R, A survey of available tools and web servers for analysis of protein-protein interactions and interfaces, Briefings in Bioinformatics, Volume: 10 Issue: 3 Pages: 217-232, 2009.

2008

  • Gursoy A, Keskin O, Nussinov R., Topological properties of protein interaction networks from a structural perspectiveBiochemical Society Transactions, Volume: 36 Pages: 1398-1403, 2008
  • Tuncbag N, Gursoy A, Guney E, Keskin O, Nussinov R, Architectures and functional coverage of protein-protein interfacesJournal of Molecular Biology, Volume: 381 Issue: 3 Pages: 785-802, 2008
  • Keskin, O,  Tuncbag, N,  Gursoy, A, Characterization and prediction of protein interfaces to infer protein-protein interaction networksCurrent Pharmaceutical Biotechnology, (9)2, 67-76, 2008.
  • Guney, E, Tuncbag, N, Keskin, O, Gursoy, A, HotSprint: database of computational hot spots in protein interfaces, Nucleic Acid Research, (36)  D662-D666, 2008.
  • O. Keskin, A. Gursoy,, B. Ma, R. Nussinov, Principles of protein-protein interactions: What are the preferred ways for proteins to interact?,Chemical Reviews, (108) 4, 1225-1244, 2008.

2007

  • Keskin O, Gursoy A, Ma B, Nussinov R. Towards drugs targeting multiple proteins in a systems biology approach,  Current Topics in Medicinal Chemistry 7 (10): 943-951 2007
  • L. Ormeci, A. Gursoy, G. Tunca, B. Erman, Computational Basis of Knowledge-Based Conformational Probabilities Derived from Local and Long-Range Interactions in ProteinsProteins: Structure, Function, and Bioinformatics, 66(1):29-40 , 2007.

2006

  • A. Gursoy, O. Keskin, M. Turkay, B. Erman, Relationships between Unfolded Configurations of Proteins and Dynamics of Folding to the Native StateJournal of Polymer Science Part B: Polymer Physics, Vol. 44, 3667-3678, 2006
  • O. Yogurtcu, E. Erzin, and A. Gursoy, Extracting Gene Regulation Information from Microarray Time-Series Data Using Hidden Markov ModelLNCS Vol.:4263 , Pages:144-153 , 2006, Springer-Verlag

2005

  • U. Ogmen, O. Keskin, S. Aytuna, R.Nussinoiv, A.Gursoy, PRISM: Protein interactions by Structural MatchingNucleic Acids Research, Vol. 33, Web server issue, pp.W331-W336, (2005). PRISM Web Server
  • A.S. Aytuna, A.Gursoy, O.Keskin, Predictions of protein-protein interactions by combining structure and sequence conservation in protein interfacesBioinformatics, Vol. 21. No. 12, pp. 2850-2855, 2005.

2004

  • A. Palazoglu, A. Gursoy, Y. Arkun and  B. Erman, Folding Dynamics of Proteins from Denatured to Native State: Principal Component Analysis, Journal of Computational Biology Dec 2004, Vol. 11, No. 6: 1149-1168.
  • O. Keskin, D. Yuret, A. Gursoy, M. Turkay and B. Erman, Relationships between amino acid sequence and backbone torsion angle preferencesProteins: Structure, Function, and Bioinformatics, Vol 55 No 4 pp. 992-998, 2004.

2003

  • A. Kocatas, A. Gursoy, R. Cetin-Atalay, Application of Data Mining Techniques to Protein-Protein Interactions“, LNCS Vol 2869 pp. 316-323, 2003  (ISCIS 2003)